9AA-vs-DAN-optimization

Parameter Optimization Report

Project description: Comparison between DAN and 9AA matrices using HeLa cells (HeLa control and HeLa + 2DG). For 9AA:

• methanol instead of ACN (the rest of parameters are the same as DAN)
• mass spec is tuned based on glu, gln
• laser focus was good
• attn tuned to get good response

Date: 2022-10-23

Config: ./param_optimization/mans_opt_9AA_config.yml

Notebook version: 0.1

List of datasets

Optimization keys: ['Matrix']

Biological key: Treatment

Batch key: ['Matrix'] (data with different batch_keys will be processed separately)

	Unnamed: 0	Run Order	Slide Position	Matrix	Slide Replicate	Cell Line	Treatment	datasetId	Problems	mask	Batch	generated-replicate-name
0	0	1	C7	DAN	1	HeLa	2DG	2022-10-13_15h14m23s	nan	0	DAN	1-C7
1	1	2	D2	DAN	1	NIH	Control	2022-10-13_15h17m59s	nan	1	DAN	1-D2
2	2	3	B5	DAN	1	HeLa	Control	2022-10-13_14h55m13s	nan	0	DAN	1-B5
3	3	4	B7	DAN	1	HeLa	2DG	2022-10-13_15h06m50s	nan	0	DAN	1-B7
4	4	5	C4	DAN	1	NIH	2DG	2022-10-13_15h08m06s	nan	1	DAN	1-C4
5	5	6	A3	DAN	1	NIH	2DG	2022-10-13_14h43m00s	nan	1	DAN	1-A3
6	6	7	A6	DAN	1	HeLa	Control	2022-10-13_14h44m58s	nan	0	DAN	1-A6
7	7	8	D7	DAN	1	HeLa	2DG	2022-10-13_15h22m42s	nan	0	DAN	1-D7
8	8	9	B2	DAN	1	NIH	Control	2022-10-13_14h52m47s	nan	1	DAN	1-B2
9	9	10	D3	DAN	1	NIH	2DG	2022-10-13_15h19m13s	nan	1	DAN	1-D3
10	10	11	C6	DAN	1	HeLa	Control	2022-10-13_15h10m58s	Wrong focus	0	DAN	1-C6
11	11	12	A2	DAN	1	NIH	Control	2022-10-13_14h39m04s	Only 1/3 finished (instrument crash)	1	DAN	1-A2
12	12	13	nan	DAN	1	nan	Control	2022-10-13_15h26m35s	Blank	1	DAN	1-nan
13	13	14	C8	9AA	2	HeLa	2DG	2022-10-14_15h42m22s	nan	0	9AA	2-C8
14	14	15	D4	9AA	2	NIH	2DG	2022-10-14_15h43m59s	nan	1	9AA	2-D4
15	15	16	D8	9AA	2	HeLa	2DG	2022-10-14_15h49m41s	nan	0	9AA	2-D8
16	16	17	A2	9AA	2	NIH	Control	2022-10-14_15h32m08s	nan	1	9AA	2-A2
17	17	18	C3	9AA	2	NIH	2DG	2022-10-14_15h39m03s	nan	1	9AA	2-C3
18	18	19	A3	9AA	2	NIH	2DG	2022-10-14_15h33m40s	nan	1	9AA	2-A3
19	19	20	D6	9AA	2	HeLa	Control	2022-10-14_15h46m09s	nan	0	9AA	2-D6
20	20	21	B6	9AA	2	HeLa	Control	2022-10-14_15h34m36s	nan	0	9AA	2-B6
21	21	22	C1	9AA	2	NIH	Control	2022-10-14_15h36m37s	nan	1	9AA	2-C1
22	22	23	D7	9AA	2	HeLa	2DG	2022-10-14_15h47m35s	nan	0	9AA	2-D7
23	23	24	C6	9AA	2	HeLa	Control	2022-10-14_15h40m19s	nan	0	9AA	2-C6
24	24	25	C2	9AA	2	NIH	Control	2022-10-14_15h37m31s	nan	1	9AA	2-C2
25	25	26	A7	DAN	3	HeLa	2DG	2022-10-14_16h01m07s	nan	0	DAN	3-A7
26	26	27	B5	DAN	3	HeLa	Control	2022-10-14_16h04m39s	nan	0	DAN	3-B5
27	27	28	C6	DAN	3	HeLa	Control	2022-10-14_16h08m17s	nan	0	DAN	3-C6
28	28	29	D8	DAN	3	HeLa	2DG	2022-10-14_16h11m10s	nan	0	DAN	3-D8
29	29	30	A7	9AA	4	HeLa	2DG	2022-10-14_17h40m40s	nan	0	9AA	4-A7
30	30	31	B5	9AA	4	HeLa	Control	2022-10-14_17h42m08s	nan	0	9AA	4-B5
31	31	32	nan	9AA	4	nan	Control	2022-10-14_19h28m32s	Blank	1	9AA	4-nan

'datasetId'

Replicate coverage

---

PCA pixel analysis

When doing PCA and DE analysis, datasets belonging to the same batch are loaded together using an 'inner join': in other words, we only keep metabolites/annotations that are present in ALL datasets of a given batch. This is done to avoid artifacts in PCA analysis and volcano plots.

In general, keep in mind the following points:

• PCA distances between conditions and replicates are comparable for datasets belonging to the same batch. Thus, you should try to put as many datasets as you can in the same batch.
• However, when annotations of certain datasets are very different (e.g. because you acquired the data using different matrices), then you should consider putting them in a separate batch. Otherwise, not many common metabolites will be left after the 'inner join' done during loading.
• If you notice that not many metabolites are left, then you could consider defining different batches or creating a custom database (see more info here)

Number of intra-cell pixels and ions left after loading (before and after filtering):

	Batch	Unique pixels	Unique ions
0	9AA	5120/5120	134/134
1	DAN	6401/6401	198/198

PCA plots

PCA distances

Intra-label vs. inter-label distance

The size of the circles represents PCA distances (the bigger the circle, the larger the distance):

• The size of the colored circles represents the distance between the two biological conditions
• The size of the empty circle with solid contour represents the distance between replicates of Control. If the circle is not present, it means that there was only one replicate available
• The size of the empty circle with dotted contour represents the distance between replicates of 2DG. If the circle is not present, it means there was only one replicate available
• You should only compare the size of circles with the same color (i.e. in the same batch), because PCA distances are not comparable between batches.

The best scenario is when both empty circles are inside the colored circle (i.e. the difference between replicates is smaller as compared to the difference between biological conditions).

---

Differential analysis and volcano plots

---

Markers intensities:

To show marker intensities, all datasets are loaded again using an 'outer' join: in other words, all annotations/metabolites that appear at least in one dataset are preserved; and if a metabolite is missing in some of the datasets, its intensity will be set to zero.

Markers found in at least one of the datasets (in alphabetical order):

	Marker name	Formula and link to plots
0	AMP	C10H14N5O7P+Cl
1	AMP	C10H14N5O7P-H
2	Adenine	C5H5N5-H
3	Glutathione	C10H17N3O6S+Cl
4	Glutathione	C10H17N3O6S-H
5	Guanine	C5H5N5O-H
6	Uracil	C4H4N2O2-H
7	aspartate	C4H7NO4-H
8	aspartate	C4H7NO4+Cl
9	citrate	C6H8O7-H
10	fructose-bisphosphate	C6H14O12P2-H
11	fumarate	C4H4O4-H
12	fumarate	C4H4O4+Cl
13	glucose	C6H12O6-H
14	glucose	C6H12O6+Cl
15	glucose-phosphate	C6H13O9P-H
16	glutamate	C5H9NO4-H
17	glutamate	C5H9NO4+Cl
18	malate	C4H6O5+Cl
19	malate	C4H6O5-H
20	oleate	C18H34O2-H
21	palmitate	C16H32O2-H
22	succinate	C4H6O4-H
23	succinate	C4H6O4+Cl
24	taurine	C2H7NO3S+Cl
25	taurine	C2H7NO3S-H
26	threonine	C4H9NO3+Cl
27	threonine	C4H9NO3-H

---

Marker: C10H14N5O7P+Cl, AMP

Go back to index list of all found markers

Raw intensities (C10H14N5O7P+Cl, AMP)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C10H14N5O7P+Cl, AMP)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C10H14N5O7P+Cl, AMP)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C10H14N5O7P-H, AMP

Go back to index list of all found markers

Raw intensities (C10H14N5O7P-H, AMP)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C10H14N5O7P-H, AMP)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C10H14N5O7P-H, AMP)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C5H5N5-H, Adenine

Go back to index list of all found markers

Raw intensities (C5H5N5-H, Adenine)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C5H5N5-H, Adenine)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C5H5N5-H, Adenine)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C10H17N3O6S+Cl, Glutathione

Go back to index list of all found markers

Raw intensities (C10H17N3O6S+Cl, Glutathione)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C10H17N3O6S+Cl, Glutathione)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C10H17N3O6S+Cl, Glutathione)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C10H17N3O6S-H, Glutathione

Go back to index list of all found markers

Raw intensities (C10H17N3O6S-H, Glutathione)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C10H17N3O6S-H, Glutathione)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C10H17N3O6S-H, Glutathione)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C5H5N5O-H, Guanine

Go back to index list of all found markers

Raw intensities (C5H5N5O-H, Guanine)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C5H5N5O-H, Guanine)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C5H5N5O-H, Guanine)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C4H4N2O2-H, Uracil

Go back to index list of all found markers

Raw intensities (C4H4N2O2-H, Uracil)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H4N2O2-H, Uracil)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H4N2O2-H, Uracil)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C4H7NO4-H, aspartate

Go back to index list of all found markers

Raw intensities (C4H7NO4-H, aspartate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H7NO4-H, aspartate)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H7NO4-H, aspartate)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C4H7NO4+Cl, aspartate

Go back to index list of all found markers

Raw intensities (C4H7NO4+Cl, aspartate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H7NO4+Cl, aspartate)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H7NO4+Cl, aspartate)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C6H8O7-H, citrate

Go back to index list of all found markers

Raw intensities (C6H8O7-H, citrate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C6H8O7-H, citrate)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C6H8O7-H, citrate)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C6H14O12P2-H, fructose-bisphosphate

Go back to index list of all found markers

Raw intensities (C6H14O12P2-H, fructose-bisphosphate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C6H14O12P2-H, fructose-bisphosphate)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C6H14O12P2-H, fructose-bisphosphate)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C4H4O4-H, fumarate

Go back to index list of all found markers

Raw intensities (C4H4O4-H, fumarate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H4O4-H, fumarate)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H4O4-H, fumarate)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C4H4O4+Cl, fumarate

Go back to index list of all found markers

Raw intensities (C4H4O4+Cl, fumarate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H4O4+Cl, fumarate)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H4O4+Cl, fumarate)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C6H12O6-H, glucose

Go back to index list of all found markers

Raw intensities (C6H12O6-H, glucose)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C6H12O6-H, glucose)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C6H12O6-H, glucose)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C6H12O6+Cl, glucose

Go back to index list of all found markers

Raw intensities (C6H12O6+Cl, glucose)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C6H12O6+Cl, glucose)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C6H12O6+Cl, glucose)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C6H13O9P-H, glucose-phosphate

Go back to index list of all found markers

Raw intensities (C6H13O9P-H, glucose-phosphate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C6H13O9P-H, glucose-phosphate)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C6H13O9P-H, glucose-phosphate)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C5H9NO4-H, glutamate

Go back to index list of all found markers

Raw intensities (C5H9NO4-H, glutamate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C5H9NO4-H, glutamate)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C5H9NO4-H, glutamate)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C5H9NO4+Cl, glutamate

Go back to index list of all found markers

Raw intensities (C5H9NO4+Cl, glutamate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C5H9NO4+Cl, glutamate)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C5H9NO4+Cl, glutamate)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C4H6O5+Cl, malate

Go back to index list of all found markers

Raw intensities (C4H6O5+Cl, malate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H6O5+Cl, malate)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H6O5+Cl, malate)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C4H6O5-H, malate

Go back to index list of all found markers

Raw intensities (C4H6O5-H, malate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H6O5-H, malate)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H6O5-H, malate)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C18H34O2-H, oleate

Go back to index list of all found markers

Raw intensities (C18H34O2-H, oleate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C18H34O2-H, oleate)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C18H34O2-H, oleate)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C16H32O2-H, palmitate

Go back to index list of all found markers

Raw intensities (C16H32O2-H, palmitate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C16H32O2-H, palmitate)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C16H32O2-H, palmitate)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C4H6O4-H, succinate

Go back to index list of all found markers

Raw intensities (C4H6O4-H, succinate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H6O4-H, succinate)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H6O4-H, succinate)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C4H6O4+Cl, succinate

Go back to index list of all found markers

Raw intensities (C4H6O4+Cl, succinate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H6O4+Cl, succinate)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H6O4+Cl, succinate)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C2H7NO3S+Cl, taurine

Go back to index list of all found markers

Raw intensities (C2H7NO3S+Cl, taurine)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C2H7NO3S+Cl, taurine)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C2H7NO3S+Cl, taurine)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C2H7NO3S-H, taurine

Go back to index list of all found markers

Raw intensities (C2H7NO3S-H, taurine)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C2H7NO3S-H, taurine)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C2H7NO3S-H, taurine)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C4H9NO3+Cl, threonine

Go back to index list of all found markers

Raw intensities (C4H9NO3+Cl, threonine)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H9NO3+Cl, threonine)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H9NO3+Cl, threonine)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

---

Marker: C4H9NO3-H, threonine

Go back to index list of all found markers

Raw intensities (C4H9NO3-H, threonine)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H9NO3-H, threonine)

Go back to index list of all found markers

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H9NO3-H, threonine)

Go back to index list of all found markers

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets: